Insights into the Effect of Soil pH on N2O and N2 Emissions and Denitrifier Community Size and Activity

ABSTRACT The objective of this study was to investigate how changes in soil pH affect the N2O and N2 emissions, denitrification activity, and size of a denitrifier community. We established a field experiment, situated in a grassland area, which consisted of three treatments which were repeatedly amended with a KOH solution (alkaline soil), an H2SO4 solution (acidic soil), or water (natural pH soil) over 10 months. At the site, we determined field N2O and N2 emissions using the 15N gas flux method and collected soil samples for the measurement of potential denitrification activity and quantification of the size of the denitrifying community by quantitative PCR of the narG, napA, nirS, nirK, and nosZ denitrification genes. Overall, our results indicate that soil pH is of importance in determining the nature of denitrification end products. Thus, we found that the N2O/(N2O + N2) ratio increased with decreasing pH due to changes in the total denitrification activity, while no changes in N2O production were observed. Denitrification activity and N2O emissions measured under laboratory conditions were correlated with N fluxes in situ and therefore reflected treatment differences in the field. The size of the denitrifying community was uncoupled from in situ N fluxes, but potential denitrification was correlated with the count of NirS denitrifiers. Significant relationships were observed between nirS, napA, and narG gene copy numbers and the N2O/(N2O + N2) ratio, which are difficult to explain. However, this highlights the need for further studies combining analysis of denitrifier ecology and quantification of denitrification end products for a comprehensive understanding of the regulation of N fluxes by denitrification.

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Denitrification activity in sediment surrounding polychaete (Ceratonereis aequisetis) burrows

Marine and Freshwater Research ◽

10.1071/mf00059 ◽

2002 ◽

Vol 53 (1) ◽

pp. 35 ◽

Cited By ~ 5

Author(s):

Robert J. De Roach ◽

Andrew W. Rate ◽

Brenton Knott ◽

Peter M. Davies

Keyword(s):

Sediment Cores ◽

River Estuary ◽

N2o Reduction ◽

Spatial Profile ◽

Potential Denitrification ◽

Burrow Wall ◽

Radial Depth ◽

Denitrification Activity ◽

Swan River

The effect of burrow-dwelling fauna on sediment denitrification within the Swan River Estuary, Western Australia, was assessed by determining the spatial profile of potential denitrification activity surrounding individual burrows of a polychaete. This activity was described for Ceratonereis aequisetis and compared with uninhabited sediment. Potential porewater denitrification activity was measured as N’2O production in the presence of acetylene (which blocks N2O reduction and NH4+ oxidation) and supplementary NO3-(provided as a substrate for denitrification). Snap-freezing of sediment cores in liquid nitrogen allowed easy sectioning in both the vertical (perpendicular depth from surface sediment) and radial (depth from burrow wall) planes. Overall, potential denitrification activity was significantly greater in inhabited sediment than in uninhabited sediment, although uninhabited sediment had higher surficial (0–10 mm) potential denitrification activity. Potential denitrification activity was also greater closer to the burrow wall (0–9 mm) rather than further into the sediment (9–13 mm). Greater sampling resolution would be required to determine whether a thin oxygenated surface layer (of either the vertical or radial plane) exists in which denitrification is inhibited. Although this study accurately demonstrates the spatial effect of C. aequisetis on sediment potential denitrification, the reported denitrification intensity may not reflect the rate in situ.

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Alkaline soil pH affects bulk soil, rhizosphere and root endosphere microbiomes of plants growing in a Sandhills ecosystem

FEMS Microbiology Ecology ◽

10.1093/femsec/fiab028 ◽

2021 ◽

Vol 97 (4) ◽

Author(s):

Lucas Dantas Lopes ◽

Jingjie Hao ◽

Daniel P Schachtman

Keyword(s):

Microbial Communities ◽

Plant Species ◽

Soil Ph ◽

Soil Microbial Communities ◽

Bulk Soil ◽

Strong Impact ◽

Alkaline Soil ◽

Alkaline Soils ◽

Soil Microbial ◽

Soil Rhizosphere

ABSTRACT Soil pH is a major factor shaping bulk soil microbial communities. However, it is unclear whether the belowground microbial habitats shaped by plants (e.g. rhizosphere and root endosphere) are also affected by soil pH. We investigated this question by comparing the microbial communities associated with plants growing in neutral and strongly alkaline soils in the Sandhills, which is the largest sand dune complex in the northern hemisphere. Bulk soil, rhizosphere and root endosphere DNA were extracted from multiple plant species and analyzed using 16S rRNA amplicon sequencing. Results showed that rhizosphere, root endosphere and bulk soil microbiomes were different in the contrasting soil pH ranges. The strongest impact of plant species on the belowground microbiomes was in alkaline soils, suggesting a greater selective effect under alkali stress. Evaluation of soil chemical components showed that in addition to soil pH, cation exchange capacity also had a strong impact on shaping bulk soil microbial communities. This study extends our knowledge regarding the importance of pH to microbial ecology showing that root endosphere and rhizosphere microbial communities were also influenced by this soil component, and highlights the important role that plants play particularly in shaping the belowground microbiomes in alkaline soils.

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Insulin-like Growth Factor Receptor 1 (IGF1R) Gene Copy Number Is Associated With Survival in Operable Non–Small-Cell Lung Cancer: A Comparison Between IGF1R Fluorescent In Situ Hybridization, Protein Expression, and mRNA Expression

Journal of Clinical Oncology ◽

10.1200/jco.2009.24.6611 ◽

2010 ◽

Vol 28 (13) ◽

pp. 2174-2180 ◽

Cited By ~ 89

Author(s):

Rafal Dziadziuszko ◽

Daniel T. Merrick ◽

Samir E. Witta ◽

Adelita D. Mendoza ◽

Barbara Szostakiewicz ◽

...

Keyword(s):

Gene Expression ◽

Growth Factor ◽

Protein Expression ◽

Squamous Cell ◽

Copy Number ◽

Gene Copy Number ◽

Growth Factor Receptor ◽

Gene Copy ◽

Cell Versus

PurposeThe purpose of this study was to characterize insulin-like growth factor-1 receptor (IGF1R) protein expression, mRNA expression, and gene copy number in surgically resected non–small-cell lung cancers (NSCLC) in relation to epidermal growth factor receptor (EGFR) protein expression, patient characteristics, and prognosis.Patients and MethodsOne hundred eighty-nine patients with NSCLC who underwent curative pulmonary resection were studied (median follow-up, 5.3 years). IGF1R protein expression was evaluated by immunohistochemistry (IHC) with two anti-IGF1R antibodies (n = 179). EGFR protein expression was assessed with PharmDx kit. IGF1R gene expression was evaluated using quantitative reverse transcription polymerase chain reaction (qRT-PCR) from 114 corresponding fresh-frozen samples. IGF1R gene copy number was assessed by fluorescent in situ hybridization using customized probes (n = 181).ResultsIGF1R IHC score was higher in squamous cell carcinomas versus other histologies (P < .001) and associated with stage (P = .03) but not survival (P = .46). IGF1R and EGFR protein expression showed significant correlation (r = 0.30; P < .001). IGF1R gene expression by qRT-PCR was higher in squamous cell versus other histologies (P = .006) and did not associate with other clinical features nor survival (P = .73). Employing criteria previously established for EGFR copy number, patients with IGF1R amplification/high polysomy (n = 48; 27%) had 3-year survival of 58%, patients with low polysomy (n = 87; 48%) had 3-year survival of 47% and patients with trisomy/disomy (n = 46; 25%) had 3-year survival of 35%, respectively (P = .024). Prognostic value of high IGF1R gene copy number was confirmed in multivariate analysis.ConclusionIGF1R protein expression is higher in squamous cell versus other histologies and correlates with EGFR expression. IGF1R protein and gene expression does not associate with survival, whereas high IGF1R gene copy number harbors positive prognostic value.

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Potential denitrification activity response to long-term nitrogen fertilization - A global meta-analysis

Journal of Cleaner Production ◽

10.1016/j.jclepro.2022.130451 ◽

2022 ◽

pp. 130451

Author(s):

Longcheng Li ◽

Mengying Yang ◽

Jincheng Li ◽

Bol Roland ◽

Zhangliu Du ◽

...

Keyword(s):

Nitrogen Fertilization ◽

Meta Analysis ◽

Potential Denitrification ◽

Activity Response ◽

Denitrification Activity

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A New Calibration Free pH-Probe for In Situ Measurements of Soil pH

Electroanalysis ◽

10.1002/elan.200403059 ◽

2004 ◽

Vol 16 (24) ◽

pp. 2058-2064 ◽

Cited By ~ 9

Author(s):

Heike Kahlert ◽

Tim Steinhardt ◽

J�rgen Behnert ◽

Fritz Scholz

Keyword(s):

Soil Ph ◽

In Situ Measurements ◽

Ph Probe ◽

Calibration Free

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Effects of Long-Term Storage on the Detection of Proteins, DNA, and mRNA in Tissue Microarray Slides

Journal of Histochemistry & Cytochemistry ◽

10.1369/0022155411423779 ◽

2011 ◽

Vol 59 (12) ◽

pp. 1113-1121 ◽

Cited By ~ 35

Author(s):

Christina Karlsson ◽

Mats G. Karlsson

Keyword(s):

Gene Copy Number ◽

Tissue Microarrays ◽

Storage Conditions ◽

Gene Copy ◽

Histological Techniques ◽

Long Term Storage ◽

Term Storage ◽

Formalin Fixed

Storage of tissue slides has been claimed to induce dramatically reduced antigen detection particularly for immunohistochemistry (IHC). With tissue microarrays, the necessity to serially cut blocks in order to obtain as much material as possible is obvious. The presumed adverse effect of storage might hamper such an approach. The authors designed an experimental setting consisting of four different storage conditions with storage time of tissue slides of up to 1 year. Detection of proteins, DNA, and mRNA was performed using IHC and in situ hybridization techniques. Slight but significant changes in IHC occurred over time. The most important factor is the primary antibody used: four showed no significant changes, whereas limited decreases in 8 antibodies could be detected by image analysis. Whether the antigen was nuclear or cytoplasmic/membranous did not matter. No major differences between different storage conditions could be shown, but storage at 4C was overall the best procedure. Furthermore, gene copy number aberrations, chromosomal translocations, and the presence of mRNA could be detected on slides stored up to 1 year. In conclusion, in tissues optimally formalin fixed and using modern histological techniques, only minute changes in tissue antigenicity are induced by long-term storage.

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In situ analysis of FGFR2 mRNA and comparison with FGFR2 gene copy number by dual-color in situ hybridization in a large cohort of gastric cancer patients

Gastric Cancer ◽

10.1007/s10120-017-0758-x ◽

2017 ◽

Vol 21 (3) ◽

pp. 401-412 ◽

Cited By ~ 4

Author(s):

Yasutoshi Kuboki ◽

Christoph A. Schatz ◽

Karl Koechert ◽

Sabine Schubert ◽

Janine Feng ◽

...

Keyword(s):

Gastric Cancer ◽

In Situ Hybridization ◽

Cancer Patients ◽

Copy Number ◽

Gene Copy Number ◽

In Situ Analysis ◽

Gene Copy ◽

Fgfr2 Gene ◽

Gastric Cancer Patients

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Soil aggregates indirectly influence litter carbon storage and release through soil pH in the highly alkaline soils of north China

PeerJ ◽

10.7717/peerj.7949 ◽

2019 ◽

Vol 7 ◽

pp. e7949 ◽

Cited By ~ 3

Author(s):

Chao Yang ◽

Jingjing Li ◽

Yingjun Zhang

Keyword(s):

Mass Loss ◽

Soil Ph ◽

North China ◽

Soil Aggregates ◽

Negative Relationship ◽

Plant Litter ◽

Leymus Chinensis ◽

Alkaline Soil ◽

Alkaline Soils ◽

Size Classes

Background Soil aggregate-size classes, structural units of soil, are the important factors regulating soil organic carbon (SOC) turnover. However, the processes of litter C mineralization and storage in different aggregates-size classes are poorly understood, especially in the highly alkaline soils of north China. Here, we ask how four different aggregate sizes influence rates of C release (Cr) and SOC storage (Cs) in response to three types of plant litter added to an un-grazed natural grassland. Methods Highly alkaline soil samples were separated into four dry aggregate classes of different sizes (2–4, 1–2, 0.25–1, and <0.25 mm). Three types of dry dead plant litter (leaf, stem, and all standing dead aboveground litter) of Leymus chinensis were added to each of the four aggregate class samples. Litter mass loss rate, Cr, and Cs were measured periodically during the 56-day incubation. Results The results showed that the mass loss in 1–2 mm aggregates was significantly greater than that in other size classes of soil aggregates on both day 28 and day 56. Macro-aggregates (1–2 mm) had the highest Cr of all treatments, whereas 0.25–1 mm aggregates had the lowest. In addition, a significant negative relationship was found between Cs/Cr and soil pH. After incubation for 28 and 56 days, the Cs was also highest in the 1–2 mm aggregates, which implied that the macro-aggregates had not only a higher CO2 release capacity, but also a greater litter C storage capacity than the micro-aggregates in the highly alkaline soils of north China.

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Techno-Economic Feasibility of In Situ Vegetable Residue Return in the Chinese Solar Greenhouse

Agronomy ◽

10.3390/agronomy11091828 ◽

2021 ◽

Vol 11 (9) ◽

pp. 1828

Author(s):

Xiaoxuan Wei ◽

Yansu Li ◽

Xiaoguang Fan ◽

Chaoxing He ◽

Yan Yan ◽

...

Keyword(s):

Bulk Density ◽

Soil Ph ◽

Sustainable Use ◽

Economic Feasibility ◽

Remarkable Increase ◽

Rotation Pattern ◽

Solar Greenhouse ◽

Final Harvest ◽

Vegetable Cultivation

The tremendous scale of protected vegetable cultivation incidentally produces considerable vegetable residue, which refers to the remaining parts of plants after the final harvest. The low use rate of vegetable residue results in nutrient waste and environmental pressure in China. In this study, we put forward vegetable residue directly returned to the soil and investigated its feasibility. Residue return was steadily conducted 5 times in a Chinese solar greenhouse with the cucumber–tomato rotation pattern. Results showed that residue return increased the soil alkali-hydrolysed nitrogen and available potassium contents by 4.97–26.22% and 9.31–21.92%, respectively, along with slightly reduced soil pH and bulk density by 1.00–5.39% and 6.72–11.81%, respectively. Gemmatimonadetes, Firmicutes, Acidobacteria, Basidiomycota, and Mortierellomycota were the major phyla with noticeable changes when residue return was conducted 5 times. Fruit yield began to obtain remarkable increase by 5.81–9.26 t·ha−1 after residue return was conducted 3 times, bringing about additional profits of 5382.0–8519.2 USD·ha−1. Residue return could cut down the disposal expense of vegetable residues by 480.89 USD·ha−1. Moreover, residue return could supplement nutrients to soil, potentially contributing to reducing chemical fertilizer inputs. In conclusion, in situ vegetable residue return could be considered to be a feasible and sustainable use technique for vegetable residues in the Chinese solar greenhouse.

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